Rosalind Franklin and the Structure of DNA

Three men, James Dewey Watson,  Francis Harry Compton Crick and Maurice Hugh Frederick Wilkins, shared the The Nobel Prize in Physiology or Medicine 1962 "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material.", that is, they  modeled DNA as a double helix, each strand of the helix has a backbone of  sugar molecules held together by phosphate groups. The two strands are twisted together and held together by hydrogen bonds. But how did they learn what DNA was made up of?

 This is where Rosalind Elsie Franklin enters the story of DNA. In 1951 she was a Research Associate at Kings College London where she worked on  X-ray diffraction studies with her colleague Maurice Wilkins. Her x-ray diffraction images of DNA led to the discovery of the DNA helix. The image on the left is known as "photograph 51" and was an x-ray diffraction image of DNA obtained by Franklin's Ph.D student Raymond Gosling.

X-ray diffraction is an instrumental technique used to elucidate the structure of crystals of chemical compounds. Incoming x-rays are diffracted by the crystal lattice and they exit the crystal at different angles. An x-ray crystallographer like Franklin can measure the angles and intensities of these diffracted x-rays to produce a 3-dimensional picture of the density of electrons in the crystal lattice. The electron density can then be used to determine the locations of atoms within the crystal lattice.

Without Franklin's knowledge, Maurice Wilkins showed this image to James Watson who used it, along with other evidence, to develop a model of DNA. Science historians still debate whether Franklin would have determined the structure of DNA on her own had her images not been shared with Watson.

Rosalind Franklin made important scientific contributions, not only to the discovery of the structure of DNA and RNA, but also in helping us to understand the structure of viruses, coal and graphite.
Unfortunately, Rosalind Franklin died of ovarian cancer in 1958. Nobel Prizes are not generally awarded posthumously so her contribution to the elucidation of the structure of DNA is not well-known.


Further Reading:
Chemistry of DNA
Intramolecular Forces
Intermolecular Forces

Suggested Study Questions:

1. Explain the terms crystalline and amorphous.
2. Give an example of a crystalline substance and an example of an amorphous substance.
3. Explain why DNA had to be crystallised before useful information could be obtained using x-ray diffraction.
4. What does the abbreviation DNA stand for?
5. What are the 4 principle bases that make up DNA?
6. These principle bases occur in pairs; what are these 2 pairs?
7. What kind of chemical bonds act between the atoms making up each base in a strand of DNA?
8. What kind of chemical forces join one of the bases on one strand of DNA to its corresponding pair on the other strand of DNA?
9. If you wanted to separate the 2 strands of a DNA double helix, what sort of chemical bonds would you need to break?
10. If you wanted to separated each base from the backbone of sugar molecules, what sort of chemical bonds would you need to break?

Hydrogen Peroxide in Space

Molecules of hydrogen peroxide, H₂O₂, have been found for the first time in interstellar space by astronomers using the European Southern Observatory-operated APEX telescope in Chile.
The hydrogen peroxide has been detected in a region of our galaxy about 400 light-years away where it is very cold (around -250^oC) and contains dense clouds of cosmic gas and dust in which new stars are being born. The clouds are mostly made of hydrogen, but contain traces of other chemicals, and are prime targets for astronomers hunting for molecules in space. The amount of hydrogen peroxide in the cloud is just one molecule for every ten billion hydrogen molecules.

Hydrogen peroxide is a key molecule for both astronomers and chemists. Its formation is closely linked to two other familiar molecules, oxygen and water, which are critical for life. Because much of the water on our planet is thought to have originally formed in space, scientists are keen to understand how it is created. Hydrogen peroxide is thought to form in space on the surfaces of cosmic dust grains, very fine particles similar to sand and soot, when hydrogen (H) is added to oxygen molecules (O₂). A further reaction of the hydrogen peroxide with more hydrogen is one way to produce water (H₂O).

Reference
P. Bergman, B. Parise, R. Liseau, B. Larsson, H. Olofsson, K. M. Menten, R. Güsten. Detection of interstellar hydrogen peroxide. Astronomy & Astrophysics, 2011; 531: L8 DOI: 10.1051/0004-6361/201117170

Further Reading
Lewis Structures (electron dot diagrams)
Intramolecular Forces
Intermolecular Forces
Temperature Conversions
Ideal Gas Calculations


Study Questions

1. Draw a Lewis Structure (electron dot diagram) for hydrogen peroxide.
2. Describe the nature of bonding that occurs within the hydrogen peroxide molecule.
3. The melting point of pure hydrogen peroxide is -0.43^oC . Explain why the melting point of pure hydrogen peroxide is slightly less than the melting point of pure water.
4. The boiling point of pure hydrogen disulfide, H₂S₂, is 70.7^oC while the boiling point of hydrogen peroxide is 150.2^oC. Explain why the boiling point of hydrogen peroxide is more than twice the boiling point of hydrogen disulfide.
5. Convert the following temperatures in ^oC to temperatures in Kelvin:
   • -250 ^oC
   • -0.43 ^oC
   • 70.1 ^oC
   • 100 ^oC
   • 150.2 ^oC
6. The amount of hydrogen peroxide in the cloud is just one molecule for every ten billion hydrogen molecules. Convert this to:
   • a concentration of hydrogen peroxide in parts per million.
   • a concentration of hydrogen peroxide in grams of hydrogen peroxide per kilogram of hydrogen
7. In outer space, 'atmospheric' pressure is about 100μPa Convert this to a pressure in:
   • kPa
   • atm
   • mmHg
   • Torr
8. Calculate the temperature of outer space if the atmospheric pressure of 100μPa is caused by the presence of 10 hydrogen molecules per cubic metre of space.
   
   
   
   

Measuring Van der Waals Forces

Van der Waals forces are among the weakest known chemical interactions, yet they are everywhere around us, making things stick together. In the world of nanotechnology, where particles can be very close together, Van der Waals forces can become the dominant interaction.

Van der Waals forces occur between atoms because, although an atom has no net overall charge, it is made up of different charged particles which are all moving and those movements cause tiny differences in charge that fluctuate very quickly. An atom that is experiencing a momentary tiny positive charge will then cause an adjacent atom to experience a momentary tiny negative charge, the oppositely charged atoms are attracted to each other.

Scientists have been studying Van der Waals forces by passing atoms through a grating. The atoms are attracted to the bars which separate the grating's slits by Van der Waals forces, and, depending on the strength of the interaction, the path the atoms are following is changed. The scientists can measure the degree to which this path has changed.

Reference
Vincent Lonij, Catherine Klauss, William Holmgren, Alexander Cronin. Atom Diffraction Reveals the Impact of Atomic Core Electrons on Atom-Surface Potentials. Physical Review Letters, 2010; 105 (23) DOI: 10.1103/PhysRevLett.105.233202

Further Reading
Intermolecular Forces
Intramolecular Forces

Study Questions

1. What is meant by the term intermolecular force?
2. How is an intermolecular force different to a intramolecular force?
3. Name three intermolecular forces.
4. Place the intermolecular forces above in order of increasing strength.
5. Name the type of intermolecular force that is predominant in interactions between molecules of:
   
• water
• paraffin wax
• methane
• ethanol (ethyl alcohol)
• trichloromethane
• nitrogen
• ammonia
• tetrachloromethane
6. For each pair of substances below, which will have the higher boiling point?
   
• octane and water
• ammonia and nitrogen
• ethanol (ethyl alcohol) and octanol
• chloromethane and methane
• hydrogen bromide and hydrogen fluoride
7. Explain why Van der Waals forces are considered to be very weak while ionic bonds, which depend on the attraction of oppositely charged ions, are considered to be very strong.
   

New Nitrogen Oxide Compound

Chemists already know about a number of compounds composed of nitrogen and oxygen:

• Nitric oxide is a colourless gas which is produced during the combustion of fossil fuels. It has a melting point of -163.6^oC, a boiling point of -150.8^oC, and rapidly oxidizes in air to form nitrogen dioxide. Its solubility in water is 7.4ml/100ml.
  
• Nitrogen dioxide is a reddish-brown toxic gas. Its melting point is -11.2^oC and its boiling point is 21.1^oC. It reacts with water to produce nitric acid.
• Nitrous oxide is a colourless gas commonly referred to as laughing gas. It is a greenhouse gas and also causes ozone depletion. Its melting point is -90.86^oC and its boiling point is -88.48^oC. Its solubility in water is 0.15g/100ml.
• Dinitrogen trioxide is a deep blue liquid at low temperatures. It has a melting point of -100.1^oC, a boiling point of 3^oC , and is very soluble in water.
• Dinitrogen tetroxide is a colourless liquid which is a powerful oxidizing agent and highly toxic. Its melting point is -11.2^oC, its boiling point is 21.1^oC, and it reacts with water to produce both nitrous aid and nitric acid.
• Dinitrogen pentoxide exists as colourless crystals. It is unstable and potentially dangerous oxidizer. It has a melting point of 30^oC and it sublimes at 47^oC. Dinitrogen pentoxide reacts with water to produce nitric acid.
  

Chemists at the Royal Institute of Technology in Sweden have discovered a new molecule in this nitrogen oxide group. The new molecule, composed only of nitrogen and oxygen, is called trinitramid. Trinitramid has the chemical formula N(NO₂)₃ and is shaped like a propeller.

Reference
Martin Rahm, Sergey V. Dvinskikh, István Furó, Tore Brinck. Experimental Detection of Trinitramide, N(NO₂)₃. Angewandte Chemie International Edition, 2011; (forthcoming)

Further Reading
Molecular Mass
Percentage Composition
Definitions of a Mole
Mass-Mole Calculations
Lewis Structures
Intermolecular Forces

Study Questions

1. Give the chemical formula for each of the following molecules:
   • nitric oxide
   • nitrogen dioxide
   • nitrous oxide
   • dinitrogen trioxide
   • dinitrogen pentoxide
2. Calculate the molecular mass (formula weight) of each of the molecules above.
3. Calculate the percentage composition of each of the molecules above.
4. Draw a Lewis Structure (electron dot diagram) for each of the molecules above.
5. Use the information in the article above, as well as your calculations, tabulate the melting points, boiling points and solubility of each molecule.
6. Graph melting points and boiling points against molecular mass.
   
7. Can you identify any trends in the melting points, boiling points, or solubilities of these molecules? Explain any trends you identify.
8. So far, scientists have only produced enough trinitramid to detect it. What do you predict its melting point, boiling point and solubility in water to be? Explain your answer.
   

Structure of Vodka

Vodka is a colourless, tasteless solution sold as an 80-proof beverage, which means it is a solution of 40% ethanol (ethyl alcohol) and 60% water. There are many different brands of Vodka at different prices, and people claim to be able to "taste" the difference. Scientists at the University of Cincinnati and the Moscow State University have been studying this phenomenon.

Dmitri Mendeleev, a Russian Chemist famous for his work on the Periodic Table, believed that a solution of 40% ethanol and 60% water would form peculiar clusters of molecules called hydrates.

Linus Pauling, a Nobel Prize winning Chemist, thought the hydrate clusters might consist of an ethanol molecule surrounded by a framework of hydrogen-bonded water molecules.

The scientists from the the Universities of Cincinnati and Moscow State analyzed the composition of 5 popular Vodka brands and found that they differed in their concentrations of ethanol hydrates. When people express a preference for one Vodka brand over another, it is not a question of "tasting" different, they appear to be perceiving the internal structure of the Vodka. Vodkas with a low concentration of ethanol hydrates might be perceived by drinkers as watery.

Reference:
Naiping Hu, Dan Wu, Kelly Cross, Sergey Burikov, Tatiana Dolenko, Svetlana Patsaeva, Dale W. Schaefer. Structurability: A Collective Measure of the Structural Differences in Vodkas. Journal of Agricultural and Food Chemistry, 2010; DOI: 10.1021/jf100609c

Study Questions:

• The concentration of beverages containing ethanol, such as spirits, are often labelled as "proof", eg, 100 proof, 80 proof. What other ways are there to express the concentration of solutions?

• Convert 80 proof to its equivalent for each of the different concentration measures you listed above.

• For the ethanol molecule, write

1. the structural formala
2. the condensed structural formula
3. molecular formula
4. empirical formula

• What is hydrogen bonding?
• Draw a diagram showing how water molecules can hydrogen bond to each other.
  

• Draw a diagram to represent an ethanol molecule surrounded by 5 hydrogen-bonded water molecules.
• At high alcohol concentration, clusters of ethanol molecules appear. What could hold these ethanol molecules together in a cage-like structure?